Many people are confused by Crimes because the film samples a lot of interconnected themes without bringing them to a satisfactory resolution. Many such themes are trite and clichéd (The compulsion of the artist to create; the interdependence between the artist and his muse; the equivalence between sex and bodily violation, between pain and orgasm), but the core of the film is the trifecta of Art, Nature and Politics. Politics seeks to control both Nature and Art, and this is not a subtext; the word "Crimes" in the title already suggests so. The National Organ Registry is erected to monitor and control the phenomenon of "accelerated evolution", because the government fears that the new human beings might pose threats to the regime. Wippet's first monologue already laid bare his reactionary politics; indeed he regards "evolution" as a dirty word. Yet later Wippet, when he tries to draw Saul, the "artist" with a revolutionary potential, to his scheme, would sing the liberal ditty of "acceptance, acknowledgement, and empowerment". Later we would learn that Saul is an undercover agent of the New Vice Unit; his job is to infiltrate underground "body art" performers and report on any suspicious activity (this poses the intriguing possibility that Saul's supernumerary organs are not "natural", but are government-induced mutations).
While the government wishes to manipulate the artist for its purpose, so do anti-establishment groups represented by the gang of plastic-eaters lead by Lang Dotrice (Scott Speedman). Dotrice wants to convince Saul and Caprice to perform a public autopsy of his murdered son, a "very special child", the first human being born to digest plastic. Dotrice knows that a if a government autopsy were performed, the record would be kept secret, hence a public art spectacle is the best way to announce the next breakthrough of human evolution. The autopsy-as-art is performed, after a tear-eyed, poignant oration by Caprice -- and the child's innards are found to be tattooed with skull-and-bone symbols and other messages of death. Doctrice suffers a mental breakdown and was swiftly murdered by (I presume) two government agents. It turns out that Timlin (Kristen Stewart's character) has replaced the child's organs, a switch-a-do that subverts the most subversive of art into propaganda and makes a cruel mockery of Caprice's pronouncement that an autopsy is "a look into oneself". Doctrice was right; now that the child's organs are taken by the government, no one will know what they are like.
Incidentally the film does not indicate that Timlin, the mousey, skittish clerk, has such technical expertise. The denouement looks like an ass-pull on Cronenberg's part, although it does mean that Timlin's amorous advances to Saul is more than sexual attraction.